"Which is harder, physics or chemistry?"
Translation:Co je těžší, fyzika nebo chemie?
Neither is correct. You can say "Který předmět je těžší...", but without that you have to use "Co" here.
Well, technically, if you were already discussing subjects and the preceding sentence did contain the word "předmět" than JanVilimek's suggestion is correct, but it is a bit too large stretch and I fear it would be confusing for most people.